Unfortunately SQL Refactor does not have a command line feature. This application only integrates as a plug-in.

The only way you can currently use the SQL Layout feature of SQL Refactor would be if you checked your code in and out of source control system into SSMS.

I know how easy it will be for you if we have command line integration.
So I have added a feature request in our internal tracking system to bring into attention of development team.Unique id for your feature request is SR-722.
I have added a watch on this issue so that I can update you if any development is going on.